1 LIN5/6 comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3). The Casal2 CppAD models have a tolerance value of 1e-9.

1.1 LIN5/6 model characteristics

The main characteristics of the Test Case LIN5/6 (ling) CASAL model are:

  • one stock, ages 3 - 25
  • one area
  • years 1972 - 2018, projection years 2019 - 2023
  • two time steps: Dec_Aug and Sep_Nov
  • two stock categories: male and female
  • natural mortality-at-age is double exponential
  • sex-specific maturity ogives specified by age
  • sex-specific von Bertalanffy age-length relationship
  • sex-specific length-weight relationship (\(W = aL^b\))
  • Beverton-Holt stock-recruitment relationship, with steepness (h) 0.84
  • ageing error
  • two surveys with sex-specific logistic selectivity
  • three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

  • survey indices
  • survey proportions-at-age
  • fishery proportions-at-age

Parameters estimated include:

  • B0
  • parameters for the natural mortality-at-age ogive
  • catchability (q) for the two surveys
  • parameters for the sex-specific selectivity curves for the two surveys
  • parameters for the sex-specific selectivity curves for the three fisheries
  • YCS (recruitment deviations)

1.2 R environment

## [1] "Tue Jul 21 11:09:46 2020"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] casal2_1.0     casal_2.30     devtools_2.3.0 usethis_1.6.1  rlist_0.4.6.1 
## [6] ggplot2_3.3.2 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.5        pillar_1.4.6      compiler_3.6.0    remotes_2.1.1    
##  [5] prettyunits_1.1.1 tools_3.6.0       testthat_2.3.2    pkgload_1.1.0    
##  [9] pkgbuild_1.1.0    digest_0.6.25     memoise_1.1.0     evaluate_0.14    
## [13] lifecycle_0.2.0   tibble_3.0.3      gtable_0.3.0      pkgconfig_2.0.3  
## [17] rlang_0.4.7       cli_2.0.2         yaml_2.2.1        xfun_0.15        
## [21] withr_2.2.0       dplyr_0.8.5       stringr_1.4.0     knitr_1.29       
## [25] desc_1.2.0        vctrs_0.3.2       fs_1.4.2          rprojroot_1.3-2  
## [29] grid_3.6.0        tidyselect_1.1.0  glue_1.4.1        data.table_1.12.8
## [33] R6_2.4.1          processx_3.4.3    fansi_0.4.1       rmarkdown_2.3    
## [37] sessioninfo_1.1.1 callr_3.4.3       purrr_0.3.4       magrittr_1.5     
## [41] backports_1.1.8   ps_1.3.3          scales_1.1.1      ellipsis_0.3.1   
## [45] htmltools_0.5.0   assertthat_0.2.1  colorspace_1.4-1  stringi_1.4.6    
## [49] munsell_0.5.0     crayon_1.3.4

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates
rownames Base_Model Sensitivity_1 Percent_Diff
q[tan_sum].q          0.09128 0.09105 0.252
q[tan_aut].q          0.12620 0.12590 0.238
initialization.B0         309000.00000 310700.00000 -0.550
natural_mortality.ogive_all1 12.49000 12.98000 -3.923
natural_mortality.ogive_all2 0.13270 0.12780 3.693
natural_mortality.ogive_all3 0.38190 0.44990 -17.806
natural_mortality.ogive_all4 0.35060 0.35390 -0.941
selectivity[surveysum_sel].male1      4.73800 4.88100 -3.018
selectivity[surveysum_sel].male2      1.75000 1.77200 -1.257
selectivity[surveysum_sel].male3      0.61000 0.60160 1.377
selectivity[surveysum_sel].female1    5.46000 5.61300 -2.802
selectivity[surveysum_sel].female2    2.20600 2.21500 -0.408
selectivity[surveyaut_sel].male1      5.50400 5.64400 -2.544
selectivity[surveyaut_sel].male2      2.31400 2.29800 0.691
selectivity[surveyaut_sel].male3      0.93920 0.93310 0.649
selectivity[surveyaut_sel].female1    5.92000 6.06200 -2.399
selectivity[surveyaut_sel].female2    2.77800 2.73800 1.440
selectivity[trawl_sel].male1      8.37000 8.40400 -0.406
selectivity[trawl_sel].male2      1.97200 1.94700 1.268
selectivity[trawl_sel].male3      61.65000 200.00000 -224.412
selectivity[trawl_sel].male4      1.04100 1.02100 1.921
selectivity[trawl_sel].female1    8.66400 8.74100 -0.889
selectivity[trawl_sel].female2    2.10000 2.08800 0.571
selectivity[trawl_sel].female3    43.31000 40.38000 6.765
selectivity[line_home_sel].male1      11.45000 8.58300 25.039
selectivity[line_home_sel].male2      8.59000 4.54700 47.066
selectivity[line_home_sel].male3      0.38010 0.26910 29.203
selectivity[line_home_sel].female1    9.61600 9.53100 0.884
selectivity[line_home_sel].female2    3.87500 3.68500 4.903
selectivity[line_spawn_sel].male1      18.30000 14.04000 23.279
selectivity[line_spawn_sel].male2      13.67000 10.01000 26.774
selectivity[line_spawn_sel].male3      1.86800 1.17300 37.206
selectivity[line_spawn_sel].female1    9.74600 9.71300 0.339
selectivity[line_spawn_sel].female2    3.00800 2.89400 3.790
recruitment.YCS1       1.00000 1.00000 0.000
recruitment.YCS2       1.00000 1.00000 0.000
recruitment.YCS3       1.00000 1.00000 0.000
recruitment.YCS4       1.00000 1.00000 0.000
recruitment.YCS5       0.48500 0.46620 3.876
recruitment.YCS6       0.45830 0.45010 1.789
recruitment.YCS7       0.56860 0.56470 0.686
recruitment.YCS8       0.56670 0.56670 0.000
recruitment.YCS9       0.48610 0.49070 -0.946
recruitment.YCS10      0.55500 0.56720 -2.198
recruitment.YCS11      0.56320 0.57880 -2.770
recruitment.YCS12      0.68760 0.71090 -3.389
recruitment.YCS13      0.62030 0.63610 -2.547
recruitment.YCS14      0.79060 0.80840 -2.251
recruitment.YCS15      0.46430 0.46930 -1.077
recruitment.YCS16      0.70080 0.70730 -0.928
recruitment.YCS17      0.41010 0.41050 -0.098
recruitment.YCS18      0.51500 0.51450 0.097
recruitment.YCS19      0.34160 0.34220 -0.176
recruitment.YCS20      0.34830 0.34730 0.287
recruitment.YCS21      0.43610 0.43820 -0.482
recruitment.YCS22      0.48060 0.47500 1.165
recruitment.YCS23      0.45220 0.45130 0.199
recruitment.YCS24      0.49170 0.49480 -0.630
recruitment.YCS25      0.46910 0.47070 -0.341
recruitment.YCS26      0.79930 0.80490 -0.701
recruitment.YCS27      0.79010 0.79210 -0.253
recruitment.YCS28      0.82610 0.83110 -0.605
recruitment.YCS29      0.70760 0.71250 -0.692
recruitment.YCS30      0.55170 0.55430 -0.471
recruitment.YCS31      0.47520 0.47680 -0.337
recruitment.YCS32      0.46170 0.46140 0.065
recruitment.YCS33      0.55500 0.55430 0.126
recruitment.YCS34      0.54670 0.54210 0.841
recruitment.YCS35      0.48320 0.48250 0.145
recruitment.YCS36      0.55020 0.54990 0.055
recruitment.YCS37      0.61530 0.61580 -0.081
recruitment.YCS38      0.77570 0.77470 0.129
recruitment.YCS39      0.63110 0.63060 0.079
recruitment.YCS40      0.77550 0.77350 0.258
recruitment.YCS41      0.64290 0.63930 0.560
recruitment.YCS42      0.70670 0.69940 1.033
recruitment.YCS43      0.65430 0.64860 0.871
recruitment.YCS44      0.51000 0.50620 0.745
recruitment.YCS45      0.58620 0.58730 -0.188
recruitment.YCS46      0.60350 0.58930 2.353
recruitment.YCS47      0.57680 0.57450 0.399
Casal2 parameter estimates
rownames betadiff_casal_flags_on betadiff_casal_flags_off betadiff_casal_flags_on_low_tol cppad_casal_flags_on cppad_casal_flags_off adolc_casal_flags_on adolc_casal_flags_off adolc_casal_flags_on_low_tol
process[Recruitment].b0               308529.00000 308529.00000 310577.00000 310576.00000 310576.00000 308529.00000 308529.00000 310577.00000
catchability[summerTANq].q                0.09137 0.09137 0.09106 0.09106 0.09106 0.09137 0.09137 0.09106
catchability[autumnTANq].q                0.12607 0.12607 0.12594 0.12594 0.12594 0.12607 0.12607 0.12594
selectivity[M_all].x0               12.49650 12.49650 12.98440 12.98440 12.98440 12.49650 12.49650 12.98440
selectivity[M_all].y0               0.13262 0.13262 0.12797 0.12797 0.12797 0.13262 0.13262 0.12797
selectivity[M_all].y1               0.38280 0.38280 0.44726 0.44727 0.44727 0.38280 0.38280 0.44726
selectivity[M_all].y2               0.35113 0.35113 0.35373 0.35373 0.35373 0.35113 0.35113 0.35373
selectivity[summerTANSel_m].a50              4.73988 4.73988 4.87645 4.87646 4.87646 4.73988 4.73988 4.87645
selectivity[summerTANSel_m].ato95            1.74459 1.74459 1.77029 1.77029 1.77029 1.74459 1.74459 1.77029
selectivity[summerTANSel_m].alpha            0.60995 0.60995 0.60184 0.60184 0.60184 0.60995 0.60995 0.60184
selectivity[summerTANSel_f].a50              5.46111 5.46111 5.60807 5.60807 5.60807 5.46111 5.46111 5.60807
selectivity[summerTANSel_f].ato95            2.20340 2.20340 2.21420 2.21419 2.21419 2.20340 2.20340 2.21420
selectivity[autumnTANSel_m].a50              5.50982 5.50982 5.63972 5.63972 5.63972 5.50982 5.50982 5.63972
selectivity[autumnTANSel_m].ato95            2.31271 2.31271 2.29781 2.29781 2.29781 2.31271 2.31271 2.29781
selectivity[autumnTANSel_m].alpha            0.94173 0.94173 0.93320 0.93319 0.93319 0.94173 0.94173 0.93320
selectivity[autumnTANSel_f].a50              5.91574 5.91574 6.05848 6.05848 6.05848 5.91574 5.91574 6.05848
selectivity[autumnTANSel_f].ato95            2.77020 2.77020 2.73846 2.73846 2.73846 2.77020 2.77020 2.73846
selectivity[trwlFSel_m].mu               8.36919 8.36919 8.40239 8.40239 8.40239 8.36919 8.36919 8.40239
selectivity[trwlFSel_m].sigma_l          1.97023 1.97023 1.94735 1.94735 1.94735 1.97023 1.97023 1.94735
selectivity[trwlFSel_m].sigma_r          61.52290 61.52290 200.00000 200.00000 200.00000 61.52290 61.52290 200.00000
selectivity[trwlFSel_m].alpha            1.04276 1.04276 1.02085 1.02085 1.02085 1.04276 1.04276 1.02085
selectivity[trwlFSel_f].mu               8.65854 8.65854 8.73949 8.73949 8.73949 8.65854 8.65854 8.73949
selectivity[trwlFSel_f].sigma_l          2.09656 2.09656 2.08849 2.08849 2.08849 2.09656 2.09656 2.08849
selectivity[trwlFSel_f].sigma_r          43.16390 43.16390 40.59470 40.59390 40.59390 43.16390 43.16390 40.59470
selectivity[lineHomeFSel_m].a50              11.45600 11.45600 8.60835 8.60828 8.60828 11.45600 11.45600 8.60835
selectivity[lineHomeFSel_m].ato95            8.59958 8.59958 4.59169 4.59155 4.59155 8.59958 8.59958 4.59169
selectivity[lineHomeFSel_m].alpha            0.38022 0.38022 0.26993 0.26993 0.26993 0.38022 0.38022 0.26993
selectivity[lineHomeFSel_f].a50              9.61476 9.61476 9.53352 9.53352 9.53352 9.61476 9.61476 9.53352
selectivity[lineHomeFSel_f].ato95            3.87014 3.87014 3.69064 3.69064 3.69064 3.87014 3.87014 3.69064
selectivity[lineSpawnFSel_m].a50              18.21510 18.21510 14.04670 14.04670 14.04670 18.21510 18.21510 14.04670
selectivity[lineSpawnFSel_m].ato95            13.59950 13.59950 10.02610 10.02600 10.02600 13.59950 13.59950 10.02610
selectivity[lineSpawnFSel_m].alpha            1.85634 1.85634 1.17449 1.17448 1.17448 1.85634 1.85634 1.17449
selectivity[lineSpawnFSel_f].a50              9.73862 9.73862 9.71478 9.71477 9.71477 9.73862 9.73862 9.71478
selectivity[lineSpawnFSel_f].ato95            2.99387 2.99387 2.89670 2.89669 2.89669 2.99387 2.99387 2.89670
process[Recruitment].ycs_values{1972} 0.48379 0.48379 0.46642 0.46642 0.46642 0.48379 0.48379 0.46642
process[Recruitment].ycs_values{1973} 0.46122 0.46122 0.45020 0.45020 0.45020 0.46122 0.46122 0.45020
process[Recruitment].ycs_values{1974} 0.56837 0.56837 0.56454 0.56453 0.56453 0.56837 0.56837 0.56454
process[Recruitment].ycs_values{1975} 0.56652 0.56652 0.56688 0.56688 0.56688 0.56652 0.56652 0.56688
process[Recruitment].ycs_values{1976} 0.48635 0.48635 0.49081 0.49080 0.49080 0.48635 0.48635 0.49081
process[Recruitment].ycs_values{1977} 0.55413 0.55413 0.56717 0.56717 0.56717 0.55413 0.55413 0.56717
process[Recruitment].ycs_values{1978} 0.56316 0.56316 0.57855 0.57854 0.57854 0.56316 0.56316 0.57855
process[Recruitment].ycs_values{1979} 0.68899 0.68899 0.71094 0.71094 0.71094 0.68899 0.68899 0.71094
process[Recruitment].ycs_values{1980} 0.62093 0.62093 0.63619 0.63619 0.63619 0.62093 0.62093 0.63619
process[Recruitment].ycs_values{1981} 0.79247 0.79247 0.80802 0.80802 0.80802 0.79247 0.79247 0.80802
process[Recruitment].ycs_values{1982} 0.46507 0.46507 0.46928 0.46928 0.46928 0.46507 0.46507 0.46928
process[Recruitment].ycs_values{1983} 0.69967 0.69967 0.70706 0.70706 0.70706 0.69967 0.69967 0.70706
process[Recruitment].ycs_values{1984} 0.40995 0.40995 0.41042 0.41042 0.41042 0.40995 0.40995 0.41042
process[Recruitment].ycs_values{1985} 0.51540 0.51540 0.51456 0.51456 0.51456 0.51540 0.51540 0.51456
process[Recruitment].ycs_values{1986} 0.34131 0.34131 0.34212 0.34211 0.34211 0.34131 0.34131 0.34212
process[Recruitment].ycs_values{1987} 0.34760 0.34760 0.34728 0.34728 0.34728 0.34760 0.34760 0.34728
process[Recruitment].ycs_values{1988} 0.43791 0.43791 0.43826 0.43826 0.43826 0.43791 0.43791 0.43826
process[Recruitment].ycs_values{1989} 0.47924 0.47924 0.47500 0.47500 0.47500 0.47924 0.47924 0.47500
process[Recruitment].ycs_values{1990} 0.45181 0.45181 0.45133 0.45133 0.45133 0.45181 0.45181 0.45133
process[Recruitment].ycs_values{1991} 0.49264 0.49264 0.49479 0.49479 0.49479 0.49264 0.49264 0.49479
process[Recruitment].ycs_values{1992} 0.46918 0.46918 0.47070 0.47070 0.47070 0.46918 0.46918 0.47070
process[Recruitment].ycs_values{1993} 0.79791 0.79791 0.80486 0.80486 0.80486 0.79791 0.79791 0.80486
process[Recruitment].ycs_values{1994} 0.79128 0.79128 0.79208 0.79208 0.79208 0.79128 0.79128 0.79208
process[Recruitment].ycs_values{1995} 0.82538 0.82538 0.83109 0.83108 0.83108 0.82538 0.82538 0.83109
process[Recruitment].ycs_values{1996} 0.70728 0.70728 0.71248 0.71248 0.71248 0.70728 0.70728 0.71248
process[Recruitment].ycs_values{1997} 0.55206 0.55206 0.55427 0.55427 0.55427 0.55206 0.55206 0.55427
process[Recruitment].ycs_values{1998} 0.47508 0.47508 0.47683 0.47683 0.47683 0.47508 0.47508 0.47683
process[Recruitment].ycs_values{1999} 0.46119 0.46119 0.46140 0.46140 0.46140 0.46119 0.46119 0.46140
process[Recruitment].ycs_values{2000} 0.55575 0.55575 0.55442 0.55442 0.55442 0.55575 0.55575 0.55442
process[Recruitment].ycs_values{2001} 0.54546 0.54546 0.54206 0.54206 0.54206 0.54546 0.54546 0.54206
process[Recruitment].ycs_values{2002} 0.48373 0.48373 0.48263 0.48263 0.48263 0.48373 0.48373 0.48263
process[Recruitment].ycs_values{2003} 0.54989 0.54989 0.54993 0.54993 0.54993 0.54989 0.54989 0.54993
process[Recruitment].ycs_values{2004} 0.61418 0.61418 0.61578 0.61578 0.61578 0.61418 0.61418 0.61578
process[Recruitment].ycs_values{2005} 0.77712 0.77712 0.77462 0.77462 0.77462 0.77712 0.77712 0.77462
process[Recruitment].ycs_values{2006} 0.63130 0.63130 0.63052 0.63052 0.63052 0.63130 0.63130 0.63052
process[Recruitment].ycs_values{2007} 0.77377 0.77377 0.77345 0.77345 0.77345 0.77377 0.77377 0.77345
process[Recruitment].ycs_values{2008} 0.64251 0.64251 0.63928 0.63928 0.63928 0.64251 0.64251 0.63928
process[Recruitment].ycs_values{2009} 0.70649 0.70649 0.69935 0.69935 0.69935 0.70649 0.70649 0.69935
process[Recruitment].ycs_values{2010} 0.65312 0.65312 0.64871 0.64871 0.64871 0.65312 0.65312 0.64871
process[Recruitment].ycs_values{2011} 0.51136 0.51136 0.50623 0.50623 0.50623 0.51136 0.51136 0.50623
process[Recruitment].ycs_values{2012} 0.58556 0.58556 0.58738 0.58738 0.58738 0.58556 0.58556 0.58738
process[Recruitment].ycs_values{2013} 0.60064 0.60064 0.58912 0.58912 0.58912 0.60064 0.60064 0.58912
process[Recruitment].ycs_values{2014} 0.57601 0.57601 0.57450 0.57448 0.57448 0.57601 0.57601 0.57450
Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on
rownames betadiff_casal_flags_on betadiff_casal_flags_off betadiff_casal_flags_on_low_tol cppad_casal_flags_on cppad_casal_flags_off adolc_casal_flags_on adolc_casal_flags_off adolc_casal_flags_on_low_tol
process[Recruitment].b0               0.000 0.000 -0.664 -0.663 -0.663 0.000 0.000 -0.664
catchability[summerTANq].q                0.000 0.000 0.344 0.344 0.344 0.000 0.000 0.344
catchability[autumnTANq].q                0.000 0.000 0.105 0.105 0.105 0.000 0.000 0.105
selectivity[M_all].x0               0.000 0.000 -3.904 -3.904 -3.904 0.000 0.000 -3.904
selectivity[M_all].y0               0.000 0.000 3.510 3.510 3.510 0.000 0.000 3.510
selectivity[M_all].y1               0.000 0.000 -16.840 -16.841 -16.841 0.000 0.000 -16.840
selectivity[M_all].y2               0.000 0.000 -0.741 -0.740 -0.740 0.000 0.000 -0.741
selectivity[summerTANSel_m].a50              0.000 0.000 -2.881 -2.882 -2.882 0.000 0.000 -2.881
selectivity[summerTANSel_m].ato95            0.000 0.000 -1.473 -1.473 -1.473 0.000 0.000 -1.473
selectivity[summerTANSel_m].alpha            0.000 0.000 1.329 1.329 1.329 0.000 0.000 1.329
selectivity[summerTANSel_f].a50              0.000 0.000 -2.691 -2.691 -2.691 0.000 0.000 -2.691
selectivity[summerTANSel_f].ato95            0.000 0.000 -0.490 -0.490 -0.490 0.000 0.000 -0.490
selectivity[autumnTANSel_m].a50              0.000 0.000 -2.358 -2.358 -2.358 0.000 0.000 -2.358
selectivity[autumnTANSel_m].ato95            0.000 0.000 0.644 0.644 0.644 0.000 0.000 0.644
selectivity[autumnTANSel_m].alpha            0.000 0.000 0.906 0.907 0.907 0.000 0.000 0.906
selectivity[autumnTANSel_f].a50              0.000 0.000 -2.413 -2.413 -2.413 0.000 0.000 -2.413
selectivity[autumnTANSel_f].ato95            0.000 0.000 1.146 1.146 1.146 0.000 0.000 1.146
selectivity[trwlFSel_m].mu               0.000 0.000 -0.397 -0.397 -0.397 0.000 0.000 -0.397
selectivity[trwlFSel_m].sigma_l          0.000 0.000 1.161 1.161 1.161 0.000 0.000 1.161
selectivity[trwlFSel_m].sigma_r          0.000 0.000 -225.082 -225.082 -225.082 0.000 0.000 -225.082
selectivity[trwlFSel_m].alpha            0.000 0.000 2.101 2.101 2.101 0.000 0.000 2.101
selectivity[trwlFSel_f].mu               0.000 0.000 -0.935 -0.935 -0.935 0.000 0.000 -0.935
selectivity[trwlFSel_f].sigma_l          0.000 0.000 0.385 0.385 0.385 0.000 0.000 0.385
selectivity[trwlFSel_f].sigma_r          0.000 0.000 5.952 5.954 5.954 0.000 0.000 5.952
selectivity[lineHomeFSel_m].a50              0.000 0.000 24.857 24.858 24.858 0.000 0.000 24.857
selectivity[lineHomeFSel_m].ato95            0.000 0.000 46.606 46.607 46.607 0.000 0.000 46.606
selectivity[lineHomeFSel_m].alpha            0.000 0.000 29.007 29.008 29.008 0.000 0.000 29.007
selectivity[lineHomeFSel_f].a50              0.000 0.000 0.845 0.845 0.845 0.000 0.000 0.845
selectivity[lineHomeFSel_f].ato95            0.000 0.000 4.638 4.638 4.638 0.000 0.000 4.638
selectivity[lineSpawnFSel_m].a50              0.000 0.000 22.884 22.884 22.884 0.000 0.000 22.884
selectivity[lineSpawnFSel_m].ato95            0.000 0.000 26.276 26.277 26.277 0.000 0.000 26.276
selectivity[lineSpawnFSel_m].alpha            0.000 0.000 36.731 36.731 36.731 0.000 0.000 36.731
selectivity[lineSpawnFSel_f].a50              0.000 0.000 0.245 0.245 0.245 0.000 0.000 0.245
selectivity[lineSpawnFSel_f].ato95            0.000 0.000 3.246 3.246 3.246 0.000 0.000 3.246
process[Recruitment].ycs_values{1972} 0.000 0.000 3.589 3.589 3.589 0.000 0.000 3.589
process[Recruitment].ycs_values{1973} 0.000 0.000 2.389 2.389 2.389 0.000 0.000 2.389
process[Recruitment].ycs_values{1974} 0.000 0.000 0.675 0.675 0.675 0.000 0.000 0.675
process[Recruitment].ycs_values{1975} 0.000 0.000 -0.064 -0.064 -0.064 0.000 0.000 -0.064
process[Recruitment].ycs_values{1976} 0.000 0.000 -0.916 -0.916 -0.916 0.000 0.000 -0.916
process[Recruitment].ycs_values{1977} 0.000 0.000 -2.353 -2.353 -2.353 0.000 0.000 -2.353
process[Recruitment].ycs_values{1978} 0.000 0.000 -2.733 -2.732 -2.732 0.000 0.000 -2.733
process[Recruitment].ycs_values{1979} 0.000 0.000 -3.185 -3.185 -3.185 0.000 0.000 -3.185
process[Recruitment].ycs_values{1980} 0.000 0.000 -2.457 -2.457 -2.457 0.000 0.000 -2.457
process[Recruitment].ycs_values{1981} 0.000 0.000 -1.962 -1.962 -1.962 0.000 0.000 -1.962
process[Recruitment].ycs_values{1982} 0.000 0.000 -0.906 -0.906 -0.906 0.000 0.000 -0.906
process[Recruitment].ycs_values{1983} 0.000 0.000 -1.056 -1.056 -1.056 0.000 0.000 -1.056
process[Recruitment].ycs_values{1984} 0.000 0.000 -0.115 -0.115 -0.115 0.000 0.000 -0.115
process[Recruitment].ycs_values{1985} 0.000 0.000 0.162 0.162 0.162 0.000 0.000 0.162
process[Recruitment].ycs_values{1986} 0.000 0.000 -0.236 -0.235 -0.235 0.000 0.000 -0.236
process[Recruitment].ycs_values{1987} 0.000 0.000 0.091 0.091 0.091 0.000 0.000 0.091
process[Recruitment].ycs_values{1988} 0.000 0.000 -0.079 -0.078 -0.078 0.000 0.000 -0.079
process[Recruitment].ycs_values{1989} 0.000 0.000 0.884 0.885 0.885 0.000 0.000 0.884
process[Recruitment].ycs_values{1990} 0.000 0.000 0.106 0.106 0.106 0.000 0.000 0.106
process[Recruitment].ycs_values{1991} 0.000 0.000 -0.436 -0.436 -0.436 0.000 0.000 -0.436
process[Recruitment].ycs_values{1992} 0.000 0.000 -0.325 -0.325 -0.325 0.000 0.000 -0.325
process[Recruitment].ycs_values{1993} 0.000 0.000 -0.871 -0.871 -0.871 0.000 0.000 -0.871
process[Recruitment].ycs_values{1994} 0.000 0.000 -0.102 -0.102 -0.102 0.000 0.000 -0.102
process[Recruitment].ycs_values{1995} 0.000 0.000 -0.691 -0.691 -0.691 0.000 0.000 -0.691
process[Recruitment].ycs_values{1996} 0.000 0.000 -0.736 -0.736 -0.736 0.000 0.000 -0.736
process[Recruitment].ycs_values{1997} 0.000 0.000 -0.400 -0.400 -0.400 0.000 0.000 -0.400
process[Recruitment].ycs_values{1998} 0.000 0.000 -0.368 -0.368 -0.368 0.000 0.000 -0.368
process[Recruitment].ycs_values{1999} 0.000 0.000 -0.045 -0.045 -0.045 0.000 0.000 -0.045
process[Recruitment].ycs_values{2000} 0.000 0.000 0.239 0.239 0.239 0.000 0.000 0.239
process[Recruitment].ycs_values{2001} 0.000 0.000 0.623 0.623 0.623 0.000 0.000 0.623
process[Recruitment].ycs_values{2002} 0.000 0.000 0.227 0.227 0.227 0.000 0.000 0.227
process[Recruitment].ycs_values{2003} 0.000 0.000 -0.008 -0.007 -0.007 0.000 0.000 -0.008
process[Recruitment].ycs_values{2004} 0.000 0.000 -0.260 -0.260 -0.260 0.000 0.000 -0.260
process[Recruitment].ycs_values{2005} 0.000 0.000 0.321 0.321 0.321 0.000 0.000 0.321
process[Recruitment].ycs_values{2006} 0.000 0.000 0.123 0.124 0.124 0.000 0.000 0.123
process[Recruitment].ycs_values{2007} 0.000 0.000 0.042 0.042 0.042 0.000 0.000 0.042
process[Recruitment].ycs_values{2008} 0.000 0.000 0.503 0.503 0.503 0.000 0.000 0.503
process[Recruitment].ycs_values{2009} 0.000 0.000 1.010 1.010 1.010 0.000 0.000 1.010
process[Recruitment].ycs_values{2010} 0.000 0.000 0.674 0.675 0.675 0.000 0.000 0.674
process[Recruitment].ycs_values{2011} 0.000 0.000 1.004 1.004 1.004 0.000 0.000 1.004
process[Recruitment].ycs_values{2012} 0.000 0.000 -0.311 -0.311 -0.311 0.000 0.000 -0.311
process[Recruitment].ycs_values{2013} 0.000 0.000 1.918 1.919 1.919 0.000 0.000 1.918
process[Recruitment].ycs_values{2014} 0.000 0.000 0.262 0.265 0.265 0.000 0.000 0.262

CASAL objective function component values
Component Base_Model Sensitivity_1
Tangaroa_bio_autumn -6.829 -6.834
Tangaroa_bio_summer -23.880 -23.960
Tangaroa_propn_at_age_aut 175.700 175.800
Tangaroa_propn_at_age_summer 835.900 835.600
longline_Campbell_home_propn_at_age 275.700 275.400
longline_Puysegur_spawn_propn_at_age 363.300 363.300
trawl_observer_propn_at_age 682.600 682.300
prior_on_q[tan_sum].q -2.364 -2.366
prior_on_q[tan_aut].q -2.033 -2.037
prior_on_initialization.B0 12.640 12.650
prior_on_natural_mortality.ogive_all 0.000 0.000
prior_on_selectivity[surveysum_sel].male 0.000 0.000
prior_on_selectivity[surveysum_sel].female 0.000 0.000
prior_on_selectivity[surveyaut_sel].male 0.000 0.000
prior_on_selectivity[surveyaut_sel].female 0.000 0.000
prior_on_selectivity[trawl_sel].male 0.000 0.000
prior_on_selectivity[trawl_sel].female 0.000 0.000
prior_on_selectivity[line_home_sel].male 0.000 0.000
prior_on_selectivity[line_home_sel].female 0.000 0.000
prior_on_selectivity[line_spawn_sel].male 0.000 0.000
prior_on_selectivity[line_spawn_sel].female 0.000 0.000
prior_on_recruitment.YCS -14.440 -14.370
clp1 0.000 0.000
clp2 0.000 0.000
clp3 0.000 0.000
YCS_average_1 0.908 0.904
Total 2297.000 2296.000
Casal2 objective function component values
rownames betadiff_casal_flags_on betadiff_casal_flags_off betadiff_casal_flags_on_low_tol cppad_casal_flags_on cppad_casal_flags_off adolc_casal_flags_on adolc_casal_flags_off adolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992                  -1.693 -1.693 -1.679 -1.679 -1.679 -1.693 -1.693 -1.679
observation->summerTANbiomass-1993                  -1.353 -1.353 -1.331 -1.331 -1.331 -1.353 -1.353 -1.331
observation->summerTANbiomass-1994                  -0.975 -0.975 -0.991 -0.991 -0.991 -0.975 -0.975 -0.991
observation->summerTANbiomass-2001                  0.430 0.430 0.354 0.354 0.354 0.430 0.430 0.354
observation->summerTANbiomass-2002                  -1.778 -1.778 -1.786 -1.786 -1.786 -1.778 -1.778 -1.786
observation->summerTANbiomass-2003                  -1.685 -1.685 -1.693 -1.693 -1.693 -1.685 -1.685 -1.693
observation->summerTANbiomass-2004                  -1.598 -1.598 -1.586 -1.586 -1.586 -1.598 -1.598 -1.586
observation->summerTANbiomass-2005                  -1.657 -1.657 -1.656 -1.656 -1.656 -1.657 -1.657 -1.656
observation->summerTANbiomass-2006                  -1.143 -1.143 -1.153 -1.153 -1.153 -1.143 -1.143 -1.153
observation->summerTANbiomass-2007                  -1.162 -1.162 -1.180 -1.180 -1.180 -1.162 -1.162 -1.180
observation->summerTANbiomass-2008                  -1.568 -1.568 -1.553 -1.553 -1.553 -1.568 -1.568 -1.553
observation->summerTANbiomass-2009                  -1.700 -1.700 -1.705 -1.705 -1.705 -1.700 -1.700 -1.705
observation->summerTANbiomass-2010                  -1.672 -1.672 -1.678 -1.678 -1.678 -1.672 -1.672 -1.678
observation->summerTANbiomass-2012                  -1.554 -1.554 -1.558 -1.558 -1.558 -1.554 -1.554 -1.558
observation->summerTANbiomass-2013                  -1.669 -1.669 -1.667 -1.667 -1.667 -1.669 -1.669 -1.667
observation->summerTANbiomass-2015                  -1.582 -1.582 -1.570 -1.570 -1.570 -1.582 -1.582 -1.570
observation->summerTANbiomass-2017                  -1.526 -1.526 -1.528 -1.528 -1.528 -1.526 -1.526 -1.528
observation->Tangaroa_propn_at_age_summer-1990                  44.218 44.218 44.393 44.393 44.393 44.218 44.218 44.393
observation->Tangaroa_propn_at_age_summer-1992                  51.993 51.993 51.753 51.753 51.753 51.993 51.993 51.753
observation->Tangaroa_propn_at_age_summer-1993                  50.200 50.200 50.168 50.168 50.168 50.200 50.200 50.168
observation->Tangaroa_propn_at_age_summer-1994                  49.743 49.743 49.785 49.785 49.785 49.743 49.743 49.785
observation->Tangaroa_propn_at_age_summer-2001                  48.355 48.355 48.237 48.237 48.237 48.355 48.355 48.237
observation->Tangaroa_propn_at_age_summer-2002                  47.830 47.830 47.879 47.879 47.879 47.830 47.830 47.879
observation->Tangaroa_propn_at_age_summer-2003                  48.442 48.442 48.620 48.620 48.620 48.442 48.442 48.620
observation->Tangaroa_propn_at_age_summer-2004                  44.823 44.823 44.865 44.865 44.865 44.823 44.823 44.865
observation->Tangaroa_propn_at_age_summer-2005                  43.097 43.097 43.117 43.117 43.117 43.097 43.097 43.117
observation->Tangaroa_propn_at_age_summer-2006                  43.891 43.891 44.058 44.058 44.058 43.891 43.891 44.058
observation->Tangaroa_propn_at_age_summer-2007                  41.848 41.848 41.841 41.841 41.841 41.848 41.848 41.841
observation->Tangaroa_propn_at_age_summer-2008                  45.225 45.225 45.267 45.267 45.267 45.225 45.225 45.267
observation->Tangaroa_propn_at_age_summer-2009                  46.844 46.844 46.806 46.806 46.806 46.844 46.844 46.806
observation->Tangaroa_propn_at_age_summer-2010                  47.128 47.128 47.202 47.202 47.202 47.128 47.128 47.202
observation->Tangaroa_propn_at_age_summer-2012                  44.353 44.353 44.183 44.183 44.183 44.353 44.353 44.183
observation->Tangaroa_propn_at_age_summer-2013                  47.251 47.251 47.021 47.021 47.021 47.251 47.251 47.021
observation->Tangaroa_propn_at_age_summer-2015                  46.473 46.473 46.342 46.342 46.342 46.473 46.473 46.342
observation->Tangaroa_propn_at_age_summer-2017                  44.182 44.182 44.082 44.082 44.082 44.182 44.182 44.082
observation->autumnTANbiomass-1992                  -1.558 -1.558 -1.572 -1.572 -1.572 -1.558 -1.558 -1.572
observation->autumnTANbiomass-1993                  -1.741 -1.741 -1.733 -1.733 -1.733 -1.741 -1.741 -1.733
observation->autumnTANbiomass-1996                  -1.779 -1.779 -1.779 -1.779 -1.779 -1.779 -1.779 -1.779
observation->autumnTANbiomass-1998                  -1.750 -1.750 -1.750 -1.750 -1.750 -1.750 -1.750 -1.750
observation->Tangaroa_propn_at_age_autumn-1992                  44.589 44.589 44.443 44.443 44.443 44.589 44.589 44.443
observation->Tangaroa_propn_at_age_autumn-1993                  45.484 45.484 45.443 45.443 45.443 45.484 45.484 45.443
observation->Tangaroa_propn_at_age_autumn-1996                  42.184 42.184 42.295 42.295 42.295 42.184 42.184 42.295
observation->Tangaroa_propn_at_age_autumn-1998                  43.464 43.464 43.610 43.610 43.610 43.464 43.464 43.610
observation->trawl_propn_at_age-1992                  36.067 36.067 35.944 35.944 35.944 36.067 36.067 35.944
observation->trawl_propn_at_age-1993                  27.516 27.516 27.476 27.476 27.476 27.516 27.516 27.476
observation->trawl_propn_at_age-1994                  25.819 25.819 25.764 25.764 25.764 25.819 25.819 25.764
observation->trawl_propn_at_age-1996                  28.394 28.394 28.397 28.397 28.397 28.394 28.394 28.397
observation->trawl_propn_at_age-1998                  24.915 24.915 24.910 24.910 24.910 24.915 24.915 24.910
observation->trawl_propn_at_age-2001                  24.580 24.580 24.542 24.542 24.542 24.580 24.580 24.542
observation->trawl_propn_at_age-2002                  26.770 26.770 26.792 26.792 26.792 26.770 26.770 26.792
observation->trawl_propn_at_age-2003                  34.564 34.564 34.511 34.511 34.511 34.564 34.564 34.511
observation->trawl_propn_at_age-2004                  29.608 29.608 29.608 29.608 29.608 29.608 29.608 29.608
observation->trawl_propn_at_age-2005                  30.147 30.147 30.166 30.166 30.166 30.147 30.147 30.166
observation->trawl_propn_at_age-2006                  33.629 33.629 33.714 33.714 33.714 33.629 33.629 33.714
observation->trawl_propn_at_age-2007                  26.635 26.635 26.588 26.588 26.588 26.635 26.635 26.588
observation->trawl_propn_at_age-2008                  27.059 27.059 27.076 27.076 27.076 27.059 27.059 27.076
observation->trawl_propn_at_age-2009                  37.213 37.213 37.237 37.237 37.237 37.213 37.213 37.237
observation->trawl_propn_at_age-2010                  30.648 30.648 30.694 30.694 30.694 30.648 30.648 30.694
observation->trawl_propn_at_age-2011                  31.266 31.266 31.260 31.260 31.260 31.266 31.266 31.260
observation->trawl_propn_at_age-2012                  32.325 32.325 32.366 32.366 32.366 32.325 32.325 32.366
observation->trawl_propn_at_age-2013                  37.072 37.072 36.943 36.943 36.943 37.072 37.072 36.943
observation->trawl_propn_at_age-2014                  30.640 30.640 30.642 30.642 30.642 30.640 30.640 30.642
observation->trawl_propn_at_age-2015                  33.456 33.456 33.474 33.474 33.474 33.456 33.456 33.474
observation->trawl_propn_at_age-2016                  36.532 36.532 36.482 36.482 36.482 36.532 36.532 36.482
observation->trawl_propn_at_age-2017                  37.755 37.755 37.708 37.708 37.708 37.755 37.755 37.708
observation->longline_Campbell_home_propn_at_age-1999                  45.348 45.348 45.256 45.256 45.256 45.348 45.348 45.256
observation->longline_Campbell_home_propn_at_age-2001                  31.965 31.965 31.950 31.950 31.950 31.965 31.965 31.950
observation->longline_Campbell_home_propn_at_age-2003                  28.644 28.644 28.675 28.675 28.675 28.644 28.644 28.675
observation->longline_Campbell_home_propn_at_age-2005                  32.750 32.750 32.776 32.776 32.776 32.750 32.750 32.776
observation->longline_Campbell_home_propn_at_age-2009                  26.033 26.033 25.611 25.611 25.611 26.033 26.033 25.611
observation->longline_Campbell_home_propn_at_age-2010                  24.302 24.302 24.461 24.461 24.461 24.302 24.302 24.461
observation->longline_Campbell_home_propn_at_age-2011                  28.878 28.878 28.935 28.935 28.935 28.878 28.878 28.935
observation->longline_Campbell_home_propn_at_age-2012                  32.258 32.258 32.389 32.389 32.389 32.258 32.258 32.389
observation->longline_Campbell_home_propn_at_age-2014                  25.495 25.495 25.357 25.357 25.357 25.495 25.495 25.357
observation->longline_Puyseger_home_propn_at_age-2000                  42.745 42.745 42.680 42.680 42.680 42.745 42.745 42.680
observation->longline_Puyseger_home_propn_at_age-2001                  31.770 31.770 31.900 31.900 31.900 31.770 31.770 31.900
observation->longline_Puyseger_home_propn_at_age-2002                  39.978 39.978 39.998 39.998 39.998 39.978 39.978 39.998
observation->longline_Puyseger_home_propn_at_age-2003                  43.527 43.527 43.511 43.511 43.511 43.527 43.527 43.511
observation->longline_Puyseger_home_propn_at_age-2004                  39.957 39.957 40.015 40.015 40.015 39.957 39.957 40.015
observation->longline_Puyseger_home_propn_at_age-2005                  25.532 25.532 25.358 25.358 25.358 25.532 25.532 25.358
observation->longline_Puyseger_home_propn_at_age-2006                  35.210 35.210 35.426 35.426 35.426 35.210 35.210 35.426
observation->longline_Puyseger_home_propn_at_age-2007                  33.981 33.981 33.782 33.782 33.782 33.981 33.981 33.782
observation->longline_Puyseger_home_propn_at_age-2008                  19.139 19.139 19.113 19.113 19.113 19.139 19.139 19.113
observation->longline_Puyseger_home_propn_at_age-2010                  24.238 24.238 24.366 24.366 24.366 24.238 24.238 24.366
observation->longline_Puyseger_home_propn_at_age-2017                  27.200 27.200 27.093 27.093 27.093 27.200 27.200 27.093
prior->B0->process[Recruitment].b0               12.640 12.640 12.646 12.646 12.646 12.640 12.640 12.646
prior->summerTANq->catchability[summerTANq].q                -2.363 -2.363 -2.365 -2.365 -2.365 -2.363 -2.363 -2.365
prior->autumnTANq->catchability[autumnTANq].q                -2.035 -2.035 -2.037 -2.037 -2.037 -2.035 -2.035 -2.037
prior->M_all_x0->selectivity[M_all].x0               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->M_all_y0->selectivity[M_all].y0               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->M_all_y1->selectivity[M_all].y1               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->M_all_y2->selectivity[M_all].y2               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[summerTANSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[autumnTANSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].mu               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].sigma_l          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].sigma_r          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_f].mu               0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_f].sigma_l          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[trwlFSel_f].sigma_r          0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineHomeFSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_m].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_m].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_m].alpha            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_f].a50              0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->selectivity[lineSpawnFSel_f].ato95            0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
prior->process[Recruitment].ycs_values{1972} -0.378 -0.378 -0.365 -0.365 -0.365 -0.378 -0.378 -0.365
prior->process[Recruitment].ycs_values{1973} -0.360 -0.360 -0.349 -0.349 -0.349 -0.360 -0.360 -0.349
prior->process[Recruitment].ycs_values{1974} -0.397 -0.397 -0.398 -0.398 -0.398 -0.397 -0.397 -0.398
prior->process[Recruitment].ycs_values{1975} -0.398 -0.398 -0.398 -0.398 -0.398 -0.398 -0.398 -0.398
prior->process[Recruitment].ycs_values{1976} -0.380 -0.380 -0.383 -0.383 -0.383 -0.380 -0.380 -0.383
prior->process[Recruitment].ycs_values{1977} -0.399 -0.399 -0.398 -0.398 -0.398 -0.399 -0.399 -0.398
prior->process[Recruitment].ycs_values{1978} -0.398 -0.398 -0.396 -0.396 -0.396 -0.398 -0.398 -0.396
prior->process[Recruitment].ycs_values{1979} -0.335 -0.335 -0.316 -0.316 -0.316 -0.335 -0.335 -0.316
prior->process[Recruitment].ycs_values{1980} -0.380 -0.380 -0.372 -0.372 -0.372 -0.380 -0.380 -0.372
prior->process[Recruitment].ycs_values{1981} -0.231 -0.231 -0.213 -0.213 -0.213 -0.231 -0.231 -0.213
prior->process[Recruitment].ycs_values{1982} -0.364 -0.364 -0.367 -0.367 -0.367 -0.364 -0.364 -0.367
prior->process[Recruitment].ycs_values{1983} -0.326 -0.326 -0.319 -0.319 -0.319 -0.326 -0.326 -0.319
prior->process[Recruitment].ycs_values{1984} -0.291 -0.291 -0.292 -0.292 -0.292 -0.291 -0.291 -0.292
prior->process[Recruitment].ycs_values{1985} -0.394 -0.394 -0.393 -0.393 -0.393 -0.394 -0.394 -0.393
prior->process[Recruitment].ycs_values{1986} -0.114 -0.114 -0.117 -0.117 -0.117 -0.114 -0.114 -0.117
prior->process[Recruitment].ycs_values{1987} -0.135 -0.135 -0.134 -0.134 -0.134 -0.135 -0.135 -0.134
prior->process[Recruitment].ycs_values{1988} -0.334 -0.334 -0.334 -0.334 -0.334 -0.334 -0.334 -0.334
prior->process[Recruitment].ycs_values{1989} -0.375 -0.375 -0.372 -0.372 -0.372 -0.375 -0.375 -0.372
prior->process[Recruitment].ycs_values{1990} -0.350 -0.350 -0.350 -0.350 -0.350 -0.350 -0.350 -0.350
prior->process[Recruitment].ycs_values{1991} -0.384 -0.384 -0.385 -0.385 -0.385 -0.384 -0.384 -0.385
prior->process[Recruitment].ycs_values{1992} -0.367 -0.367 -0.369 -0.369 -0.369 -0.367 -0.367 -0.369
prior->process[Recruitment].ycs_values{1993} -0.225 -0.225 -0.217 -0.217 -0.217 -0.225 -0.225 -0.217
prior->process[Recruitment].ycs_values{1994} -0.233 -0.233 -0.232 -0.232 -0.232 -0.233 -0.233 -0.232
prior->process[Recruitment].ycs_values{1995} -0.192 -0.192 -0.185 -0.185 -0.185 -0.192 -0.192 -0.185
prior->process[Recruitment].ycs_values{1996} -0.319 -0.319 -0.315 -0.315 -0.315 -0.319 -0.319 -0.315
prior->process[Recruitment].ycs_values{1997} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{1998} -0.372 -0.372 -0.373 -0.373 -0.373 -0.372 -0.372 -0.373
prior->process[Recruitment].ycs_values{1999} -0.360 -0.360 -0.360 -0.360 -0.360 -0.360 -0.360 -0.360
prior->process[Recruitment].ycs_values{2000} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{2001} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{2002} -0.378 -0.378 -0.377 -0.377 -0.377 -0.378 -0.378 -0.377
prior->process[Recruitment].ycs_values{2003} -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399 -0.399
prior->process[Recruitment].ycs_values{2004} -0.383 -0.383 -0.383 -0.383 -0.383 -0.383 -0.383 -0.383
prior->process[Recruitment].ycs_values{2005} -0.249 -0.249 -0.251 -0.251 -0.251 -0.249 -0.249 -0.251
prior->process[Recruitment].ycs_values{2006} -0.375 -0.375 -0.375 -0.375 -0.375 -0.375 -0.375 -0.375
prior->process[Recruitment].ycs_values{2007} -0.252 -0.252 -0.253 -0.253 -0.253 -0.252 -0.252 -0.253
prior->process[Recruitment].ycs_values{2008} -0.368 -0.368 -0.370 -0.370 -0.370 -0.368 -0.368 -0.370
prior->process[Recruitment].ycs_values{2009} -0.320 -0.320 -0.326 -0.326 -0.326 -0.320 -0.320 -0.326
prior->process[Recruitment].ycs_values{2010} -0.362 -0.362 -0.364 -0.364 -0.364 -0.362 -0.362 -0.364
prior->process[Recruitment].ycs_values{2011} -0.392 -0.392 -0.390 -0.390 -0.390 -0.392 -0.392 -0.390
prior->process[Recruitment].ycs_values{2012} -0.394 -0.394 -0.393 -0.393 -0.393 -0.394 -0.394 -0.393
prior->process[Recruitment].ycs_values{2013} -0.389 -0.389 -0.393 -0.393 -0.393 -0.389 -0.389 -0.393
prior->process[Recruitment].ycs_values{2014} -0.396 -0.396 -0.396 -0.396 -0.396 -0.396 -0.396 -0.396
additional_prior->YCS_average_1                  0.908 0.908 0.904 0.904 0.904 0.908 0.908 0.904
total_score                  2296.970 2296.970 2296.140 2296.140 2296.140 2296.970 2296.970 2296.140

## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-006"                                                                  
## [2] "fmm: have converged: t = 4.30035e-007 f = 2296.34"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 188 quasi-Newton iterations using 303 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       77"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     3003"
##  [4] "Number of Iterations....: 29"                                   
##  [5] "Number of objective function evaluations             = 52"      
##  [6] "Number of objective gradient evaluations             = 30"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 52"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 30"      
## [11] "Number of Lagrangian Hessian evaluations             = 29"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       77"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     3003"
##  [4] "Number of Iterations....: 29"                                   
##  [5] "Number of objective function evaluations             = 52"      
##  [6] "Number of objective gradient evaluations             = 30"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 52"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 30"      
## [11] "Number of Lagrangian Hessian evaluations             = 29"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)
## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## NULL
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## NULL
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others...

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.7359 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9871 0.9823"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): 0 0"

## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): 0 0"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"